[gmx-users] itp file for flavins

Justin A. Lemkul jalemkul at vt.edu
Wed May 16 00:09:18 CEST 2012

On 5/15/12 5:37 PM, vijaya subramanian wrote:
> Hi
> I found all the rtp files-aminoacid.rtp,dna.rtp but not fmnr.rtp which is in
> ffgmx.rtp according to the gromacs building blocks site.
> I need to look at the fmnr.rtp file to match atom names.

Individual molecules generally do not have their own .rtp files.  The parameters 
you need are in aminoacids.rtp:

$ grep FMN g*.ff/*.rtp
gmx.ff/aminoacids.rtp:[ FMNO ]
gmx.ff/aminoacids.rtp:[ FMNR ]
gmx.ff/aminoacids.rtp:[ FMNS ]
gromos43a1.ff/aminoacids.rtp:[ FMNO ]
gromos43a1.ff/aminoacids.rtp:[ FMNS ]
gromos43a1.ff/aminoacids.rtp:[ FMNR ]
gromos43a2.ff/aminoacids.rtp:[ FMNO ]
gromos43a2.ff/aminoacids.rtp:[ FMNS ]
gromos43a2.ff/aminoacids.rtp:[ FMNR ]
gromos45a3.ff/aminoacids.rtp:[ FMNO ]
gromos45a3.ff/aminoacids.rtp:[ FMNS ]
gromos45a3.ff/aminoacids.rtp:[ FMNR ]
gromos53a5.ff/aminoacids.rtp:[ FMNO ]
gromos53a5.ff/aminoacids.rtp:[ FMNS ]
gromos53a5.ff/aminoacids.rtp:[ FMNR ]
gromos53a6.ff/aminoacids.rtp:[ FMNO ]
gromos53a6.ff/aminoacids.rtp:[ FMNS ]
gromos53a6.ff/aminoacids.rtp:[ FMNR ]

I would recommend not using gmx.ff, for reasons described in the manual.  The 
newer versions of Gromos96 are more suitable.



Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list